Many prior art methods such as interferometers, mechanical probe profilometers, laser scanners, and confocal microscopes are used today to measure three dimensional topology of surfaces. These methods compromise between height resolution, spatial resolution, and time of measurement. Instruments that have very high height resolution have low spatial resolution or take extremely long periods of time to measure large surface areas. The present invention achieves high sub-nanometer 3D height resolution, micron spatial resolution, and can measure large surfaces, such as a 300 mm wafer, using a flat bed scanner, in a matter of minutes.